Thanks. I have made a note to try to improve this issue in a future version. I'm not sure if it will make it into v9.0 though (depends on time to look into it and implement a solution). CSE HTML Validator tries to validate raw script files with a minimum of fuss but is not designed to as its main purpose.

UPDATE: I was able to address the message about the title in the next BETA. The JavaScript message is generated by JavaScript Lint. I don't see any good solution to this. It's probably best to just ignore the message.